Solution structure of a DNA decamer containing the antiviral drug ganciclovir: Combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement

Biochemistry

Volumn 36, Issue 18, 1997, Pages 5336-5345

  Foti, Matthew ^a,b   Marshalko, Stephen ^d   Schurter, Eric ^a   Kumar, Surat ^a   Beardsley, G Peter ^d   Schweitzer, Barry I ^a,c  

^a FLORIDA HOSPITAL   (United States)

^b UNIVERSITY OF SOUTH FLORIDA   (United States)

^c UNIVERSITY OF CENTRAL FLORIDA   (United States)

^d YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIVIRUS AGENT; GANCICLOVIR;

ARTICLE; CONTROLLED STUDY; DNA STRUCTURE; DRUG DNA BINDING; DRUG STRUCTURE; MOLECULAR DYNAMICS; NUCLEAR OVERHAUSER EFFECT; PHOSPHORUS NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE;

ANTIVIRAL AGENTS; BASE COMPOSITION; CRYSTALLOGRAPHY, X-RAY; DNA; GANCICLOVIR; GLYCOSIDES; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; PHOSPHORIC ACID ESTERS; SOLUTIONS; THERMODYNAMICS;

HERPES; HERPESVIRIDAE;

EID: 0030969636     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi962604e     Document Type: Article

References (52)

1. Altona, C., & Sundaralingam, M. (1972) J. Am. Chem. Soc. 94, 8205-8212.
2. Arnott, S., & Hukins, D. W. (1972) Biophys. Biochem. Res. Commun. 47, 1504-1509.
3. Arnott, S., & Hukins, D. W. (1973) J. Mol. Biol. 81, 93-105.
4. Baleja, J. D., Pon, R. T., & Sykes, B. D. (1990) Biochemistry 29, 4828-39.
5. Borer, P. N., LaPlante, S. R., Kumar, A., Zanatta, N., Martin, A., Hakkinen, A., & Levy, G. C. (1994) Biochemistry 33, 2441-2450.
6. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., & Karplus, M. (1983) J. Comput. Chem. 74, 187-217.
7. Brunger, A. T. (1993) X-PLOR 3.1: A System for Crystallography and NMR, Yale University, New Haven, CT.
8. Buckner, F. S., & Pomeroy, C. (1993) Clin. Infect. Dis. 17, 644-656.
9. Callihan, D., West, J., Schweitzer, B. I., & Logan, T. M. (1996) J. Magn. Reson., Ser. B 112, 82-86.
10. Chen, S. H., Shine, H. D., Goodman, J. C., Grossman, R. G., & Woo, S. L. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 3054-3057.
11. Clore, G. M., Hartmut, O., McLaughlin, L. W., Benseler, F., Happ, C. S., Happ, E., & Gronenborn, A. M. (1988) Biochemistry 27, 4185-4197.
12. Culver, K. W., Ram, Z., Walbridge, S., Ishii, H., Oldfield, E. H., & Blaise, R. M. (1992) Science 256, 1550-1552.
13. Culver, K. W., Van Gilder, J., Link, C. J., Carlstrom, T., Buroker, T., Yuh, W., Koch, K., Schabold, K., Doornbas, S., Wetjen, B., & Blaise, R. M. (1994) Hum. Gene Ther. 5, 343-379.
14. Cuniasse, Ph., Sowers, L. C., Eritja, R., Kaplan, B., Goodman, M. F., Cognet, J. A. H., Le Bret, M., Guschlbauer, W., & Fazakerley, G. V. (1989) Biochemistry 28, 2018-2026.
15. DiMaio, J. M., Clary, B. M., Bia, D. F., Coveney, E., Pappas, T. N., & Lyerly, H. K. (1994) Surgery 116, 205-213.
16. Emmanuel, D. (1990) Semin. Hematol. 27, 22-27.
17. Erice, A., Jordan, M. C., Chace, B. A., Fletcher, C., Chinnock, B. J., & Balfour, H. H. (1987) JAMA, J. Am. Med. Soc. 257, 3082-3087.
18. Faulds, D., & Heel, R. C. (1990) Drugs 39, 597-638.
19. Frank, K. B., Chiou, J. F., & Cheng, Y. C. (1984) J. Biol. Chem. 259, 1566-1569.
20. Gronenborn, A. M., & Clore, G. M. (1989) Biochemistry 28, 5978-5984.
21. Hasegawa, Y., Emi, N., & Shimokata, K. (1995) J. Mol. Med. 73, 107-112.
22. Holak, T. A., Engstrom, A., Draulis, P. J., Lindeberg, G., Bennich, H., Jones, A., Gronenborn, A. M., & Clore, G. M. (1988) Biochemistry 27, 760-769.
23. Hwang, T. L., & Shaka, A. J. (1995) J. Magn. Reson. 112A, 275-279.
24. Ido, A., Nakata, K., Katau, Y., Nakao, K., Murata, K., Fujita, M., Ishii, N., Tamaoki, T., Shiku, H., & Nagataki, S. (1995) Cancer Res. 35, 3100-3109.
25. Isley, D. D., Lee, S. H., Miller, W. H., & Kucha, R. D. (1995) Biochemistry 34, 2504-2510.
26. James, T. L. (1991) Curr. Opin. Struct. Biol. 1, 1042-53.
27. Karkas, J. D., Germaershausen, J., Tolman, R. L., MacCoss, M., Wagner, A. F., Liou, R., & Bostedor, R. (1987) Biochim. Biophys. Acta 911, 127-135.
28. Kellogg, G. W., & Schweitzer, B. I. (1993) J. Biomol. NMR 3, 577-595.
29. Kim, S.-G., Lin, L.-J., & Reid, B. R. (1992) Biochemistry 31, 3564-3574.
30. Lavery, R., & Sklènar, H. (1988) J. Biomol. Struct. Dyn. 6, 63-91.
31. Lavery, R., & Sklènar, H. (1989) J. Biomol. Struct. Dyn. 6, 655-667.
32. Manome, Y., Abe, M., Hagen, M. F., Fine, H. A., & Kufe, D. W. (1994) Cancer Res. 54, 5408-5413.
33. Marshalko, S. J., Schweitzer, B. I., & Beardsley, G. P. (1995) Biochemistry 34, 9235-9248.
34. Nevins, T. E., & Dunn, D. L. (1992) J. Am. Soc. Nephrol. 2, S270-S273.
35. Nilges, M., Clore, G. M., Gronenborn, A. M., Brünger, A. T., Karplus, M., & Nilsson, L. (1987a) Biochemistry 26, 3718-3733.
36. Nilges, M., Clore, G. M., Gronenborn, A. M., Piel, N., & McLaughlin, L. W. (1987b) Biochemistry 26, 3734-3744.
37. Nilges, M., Hazabettl, J., Brünger, A. T., & Holak, T. A. (1991) J. Mol. Biol. 219, 499-510.
38. Ravishanker, R., Swaminathan, S., Beveridge, R. L., & Sklenar, H. (1989) J. Biomol. Struct. Dyn. 6, 669-699.
39. Reardon, J. E. (1989) J. Biol. Chem. 264, 7405-7411.
40. Reid, R., Mar, E. C., Huang, E. S., & Topal, M. D. (1988) J. Biol. Chem. 263, 3898-3905.
41. Rosenberg, J. M., Seeman, N. C., Day, R. O., & Rich, A. (1976) J. Mol. Biol. 104, 145-167.
42. Schweitzer, B. I., Mikita, T., Kellogg, G. W., Gardner, K. H., & Beardsley, G. P. (1994) Biochemistry 33, 11460-11475.
43. Schweitzer, B. I., Gardner, K. H., & Tucker-Kellogg, G. (1995) J. Biomol. NMR 6, 180-188.
44. Seeman, N. C., Rosenberg, J. M., Suddath, F. L., Kim, J. J. P., & Rich, A. (1976) J. Mol. Biol. 104, 109-144.
45. Smythe, W. R., Hwang, H. C., Amin, K. M., Eck, S. L., Davidson, B. L., Wilson, J. M., Kaiser, L. R., & Albelda, S. M. (1994) Cancer Res. 54, 2055-2059.
46. States, D. J., Haberkorn, R. A., & Ruben, D. J. (1982) J. Magn. Reson. 48, 286-292.
47. Thomas, P. D., Basus, V. J., & James, T. L. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 1237-1241.
48. Tolman, R. L. (1989) in Nucleotide Analogues As Antiviral Agents (Martin, J. C., Ed.) pp 35-50, American Chemical Society, Washington, DC.
49. Wüthrich, K. (1986) in NMR of Proteins and Nucleic Acids, pp 203-255, John Wiley & Sons, New York.
50. Yip, P., & Case, D. A. (1989) J. Magn. Reson. 83, 643-648.
51. Yoshida, K., Kawami, H., Yamaguchi, Y., Kuniyasu, H., Nishiyama, M., Hirai, T., Yanagihara, K., Tahara, E., & Toge, T. (1995) Cancer 75, 1467-1471.
52. Zaia, J. S. (1993) Clin. Infect. Dis. 17, S392-399.